- using R Under development (unstable) (2025-02-26 r87830)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.7 (1+b1)
Debian flang-new version 19.1.7 (1+b1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘flowTraceR/DESCRIPTION’ ... OK
- this is package ‘flowTraceR’ version ‘0.1.0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package ‘flowTraceR’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [2s/2s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
- checking whether the package can be unloaded cleanly ... [1s/2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
- checking loading without being on the library search path ... [1s/2s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [9s/12s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [3s/4s] ERROR
Running examples in ‘flowTraceR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_all_levels
> ### Title: Conversion of software specific levels
> ### Aliases: convert_all_levels
>
> ### ** Examples
>
> # Load libraries
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> library(stringr)
> library(tidyr)
> library(comprehenr)
> library(tibble)
>
> # MaxQuant example data
> evidence <- tibble::tibble(
+ "Modified sequence" = c("_AACLLPK_",
+ "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_",
+ "ALTDM(Dummy_Modification)PQMK"),
+ Charge = c(2,2,3),
+ "Protein group IDs" = c("26", "86;17", "86;17")
+ )
>
> proteingroups <- tibble::tibble(
+ "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"),
+ id = c(26, 86, 17)
+ )
>
> # Conversion
> convert_all_levels(
+ input_df = evidence,
+ input_MQ_pg = proteingroups,
+ software = "MaxQuant"
+ )
Error in unlist(., .data, use.names = FALSE) :
'recursive' must be a length-1 vector
Calls: convert_all_levels -> sort_string_pg -> %>% -> unlist
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [8s/9s] ERROR
Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(flowTraceR)
>
> test_check("flowTraceR")
[ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_conversion.R:160:3'): convert_proteingroups with MaxQuant output is succesful ──
Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "MaxQuant") at test_conversion.R:160:3
2. │ └─flowTraceR:::sort_string_pg(...)
3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ...
4. └─base::unlist(., .data, use.names = FALSE)
── Error ('test_conversion.R:178:3'): convert_proteingroups with PD output is succesful ──
Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "PD") at test_conversion.R:178:3
2. │ └─flowTraceR:::sort_string_pg(...)
3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ...
4. └─base::unlist(., .data, use.names = FALSE)
── Error ('test_conversion.R:196:3'): convert_proteingroups with DIA-NN output is succesful ──
Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "DIA-NN") at test_conversion.R:196:3
2. │ └─flowTraceR:::sort_string_pg(...)
3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ...
4. └─base::unlist(., .data, use.names = FALSE)
── Error ('test_conversion.R:214:3'): convert_proteingroups with Spectronaut output is succesful ──
Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "Spectronaut") at test_conversion.R:214:3
2. │ └─flowTraceR:::sort_string_pg(...)
3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ...
4. └─base::unlist(., .data, use.names = FALSE)
── Error ('test_conversion.R:239:3'): convert_all_levels with MaxQuant output is succesful ──
Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─flowTraceR::convert_all_levels(...) at test_conversion.R:239:3
2. │ └─flowTraceR:::sort_string_pg(...)
3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ...
4. └─base::unlist(., .data, use.names = FALSE)
── Error ('test_conversion.R:260:3'): convert_all_levels with PD output is succesful ──
Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─flowTraceR::convert_all_levels(input_df = data, software = "PD") at test_conversion.R:260:3
2. │ └─... %>% convert_precursor(software = "PD")
3. ├─flowTraceR::convert_precursor(., software = "PD")
4. │ ├─"Annotated Sequence" %in% colnames(input_df)
5. │ └─base::colnames(input_df)
6. │ └─base::is.data.frame(x)
7. ├─flowTraceR::convert_modified_peptides(., software = "PD")
8. │ ├─"Annotated Sequence" %in% colnames(input_df)
9. │ └─base::colnames(input_df)
10. │ └─base::is.data.frame(x)
11. ├─flowTraceR::convert_proteingroups(., software = "PD")
12. │ └─flowTraceR:::sort_string_pg(...)
13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ...
14. └─base::unlist(., .data, use.names = FALSE)
── Error ('test_conversion.R:278:3'): convert_all_levels with DIA-NN output is succesful ──
Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─flowTraceR::convert_all_levels(input_df = data, software = "DIA-NN") at test_conversion.R:278:3
2. │ └─... %>% convert_precursor(software = "DIA-NN")
3. ├─flowTraceR::convert_precursor(., software = "DIA-NN")
4. │ ├─"Precursor.Id" %in% colnames(input_df)
5. │ └─base::colnames(input_df)
6. │ └─base::is.data.frame(x)
7. ├─flowTraceR::convert_modified_peptides(., software = "DIA-NN")
8. │ ├─"Precursor.Id" %in% colnames(input_df)
9. │ └─base::colnames(input_df)
10. │ └─base::is.data.frame(x)
11. ├─flowTraceR::convert_proteingroups(., software = "DIA-NN")
12. │ └─flowTraceR:::sort_string_pg(...)
13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ...
14. └─base::unlist(., .data, use.names = FALSE)
── Error ('test_conversion.R:296:3'): convert_all_levels with Spectronaut output is succesful ──
Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─flowTraceR::convert_all_levels(input_df = data, software = "Spectronaut") at test_conversion.R:296:3
2. │ └─... %>% convert_precursor(software = "Spectronaut")
3. ├─flowTraceR::convert_precursor(., software = "Spectronaut")
4. │ ├─"EG.PrecursorId" %in% colnames(input_df)
5. │ └─base::colnames(input_df)
6. │ └─base::is.data.frame(x)
7. ├─flowTraceR::convert_modified_peptides(., software = "Spectronaut")
8. │ ├─"EG.PrecursorId" %in% colnames(input_df)
9. │ └─base::colnames(input_df)
10. │ └─base::is.data.frame(x)
11. ├─flowTraceR::convert_proteingroups(., software = "Spectronaut")
12. │ └─flowTraceR:::sort_string_pg(...)
13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ...
14. └─base::unlist(., .data, use.names = FALSE)
── Error ('test_utils.R:44:3'): sort_string_pg is succesful ────────────────────
Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─flowTraceR:::sort_string_pg(...) at test_utils.R:44:3
2. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ...
3. └─base::unlist(., .data, use.names = FALSE)
[ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [6s/8s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Example_RT_distribution.Rmd’ using rmarkdown
Quitting from lines 51-55 [all levels] (Example_RT_distribution.Rmd)
Error: processing vignette 'Example_RT_distribution.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘Example_RT_distribution.Rmd’
--- re-building ‘Requirements.Rmd’ using rmarkdown
--- finished re-building ‘Requirements.Rmd’
--- re-building ‘Workflow.Rmd’ using rmarkdown
Quitting from lines 97-101 [proteinGroup] (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘Workflow.Rmd’
SUMMARY: processing the following files failed:
‘Example_RT_distribution.Rmd’ ‘Workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [6s/8s] OK
- checking HTML version of manual ... [0s/1s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 3 ERRORs